Introduction to R

[NAME]

Why is R programming a useful skill?

(John Drake)

About Myself

My research interest is [INSERT DESCRIPTION]
I use R in my research to:
- organize data
- develop machine learning algorithms
I mostly work [in this disease system or approach]
My contact info is [INSERT EMAIL]

Workshop Goals

The workshop series consists of four half day workshops each focusing on a different part of the research process

Introduction to R and RStudio (Today)
Conducting reproducible research (Date; Person)
Visualizing data (Date; Person)
Simulating infectious disease dynamics (Date; Person)

workflow

Workshop Format

Introduction of instructor & how they use R
Review of past concepts
Outline of the day's goals
Work through data analysis project
Reflection on day's materials

Expectations

You

Come ready to participate
- review the materials before hand
- room tends to be cold
Ask questions
Help eachother

Instructor

Come ready to participate
Help you find answers
Be a resource for you during the REU program

Outline

You should be able to…

calculate summary statistics of a dataset
create a figure from data

Topics

What is R and RStudio?
Introduction to with tidyverse with code along

Break
Troubleshooting
Exploring data in groups
Wrap Up

1. What is R and RStudio?

R logo

R is a free, open source programming language with a pre-set functionality (base R)
Functionality is extented by R packages which are collections of functions and data sets developed by the community.

$RStudio logo$

RStudio is a software program that makes R programming easier by:
- write and test code efficiently
- orginizing files into projects
- intergrating different programming lanuguages (RMarkdown, Latex, etc.)

RStudio

Let's open today's exercise by clicking on W1_Exercise.Rproj in the W1_Exercise folder.

RStudio should automatically open from here.

RStudio

3. Introduction to tidyverse

The tidyverse is a set of packages that work in harmony because they share common design.
Unique syntax used pipes (%>%) to connect data (object) to verbs (functions).

tidy syntax

tidyverse package

The tidyverse package is designed to make it easy to install and load core packages from the tidyverse in a single command.

tidy verse package

Install tidyverse package

We need to install the tidyverse package. This can be done by clicking on buttons in Rstudio or from the console using install.packages()
Install the package by running line 21 of the W1_Exercise.Rmd file

#install all the packages in the tidyverse
install.packages("tidyverse")

Load tidyverse package

Once a package is installed, we need to load it during our current R session.
This is done using library().
How should this code be altered to load the tidyverse library?

#load tidyverse library
library()

Switch over to W1_Exercise.Rmd

Break

4. How to get unstuck: functions

Every function has a help page
?function() to access

How to get unstuck: packages

Packages have a vignette and/or reference manual on cran.r-project.org
People often make their own tutorials too

How to get unstuck: packages

Cheatsheets published out by RStudio

cheatsheets

https://www.rstudio.com/resources/cheatsheets/

How to get unstuck: packages

Cheatsheets published out by RStudio
Contributed cheatsheets

cheatsheets

How to get unstuck: error messages

error

First, try to understand the error message. It can be very helpful.

How to get unstuck: error messages

But sometimes, the messages is cryptic. So use google!

$google$

5. Exploring further

Let's work in small groups (max [X])

Develop a question about that can be answered with this data
Decide on the needed verbs, and order
Write the code in the final code chunck of the W1_Exercise.Rmd file

More instructions in the file.

6. Wrap Up

Today

dplyr package
- filter, arrange…
- ggplot2 package
- geom_point, facet…

Next

How to communicate
- others
- future self